As per this issue on the WordPress trac, the problem are the rules 4 and 5.
The solution is to change the url parameter and add 1, so, instead of this:
<rule name="WordPress Rule 4" stopProcessing="true">
<match url="^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*)" ignoreCase="false" />
<action type="Rewrite" url="{R:1}" />
</rule>
<rule name="WordPress Rule 5" stopProcessing="true">
<match url="^([_0-9a-zA-Z-]+/)?([_0-9a-zA-Z-]+/)?(.*\.php)$" ignoreCase="false" />
<action type="Rewrite" url="{R:2}" />
</rule>
You have this:
<rule name="WordPress Rule 4" stopProcessing="true">
<match url="^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*)" ignoreCase="false" />
<action type="Rewrite" url="{R:2}" />
</rule>
<rule name="WordPress Rule 5" stopProcessing="true">
<match url="^([_0-9a-zA-Z-]+/)?([_0-9a-zA-Z-]+/)?(.*\.php)$" ignoreCase="false" />
<action type="Rewrite" url="{R:3}" />
</rule>
Doing this change allows the multisite feature to work.